Senior Congress leaders, including former Prime Minister Manmohan Singh, party chief Sonia Gandhi and vice president Rahul Gandhi, also paid homage to the late leader.
Mukherjee and Singh, besides Rahul Gandhi, paid floral tributes to her at her memorial, 'Shakti Sthal'.
"No one can erase Indiraji's memory," Mukherjee said at an event later at 1 Safdarjung Road, where Indira Gandhi was assassinated by her bodyguards on October 31, 1984. A photo exhibition has been organised there to mark her 100th birth anniversary.
"She fought for secularism, against all those forces seeking to divide the Indian people on lines of religion and caste. For her as Prime Minister there was but one religion, a sacred creed passionately held-- that all Indians were equal children of the motherland," the Congress president said in her speech.
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Indira Gandhi also fought for India's dignity and independence as a sovereign nation, against the dominance of superpowers, she said.
"And not only for India, but for all countries that resisted colonial and post-colonial forms of hegemony," Sonia Gandhi added.
"I remember you Dadi with so much love and happiness. You are my mentor and guide. You give me strength. #Indira100," he tweeted.
Congress communications incharge Randeep Surjewala said on Twitter that she worked tirelessly "to shape a new future" for the country.
"...India first & India always. That was Indiraji! #Indira100," he said on the micro-blogging site.
Often described as the 'Iron Lady of India', Gandhi was born on this day in 1917 in Uttar Pradesh's Allahabad.